Biomes in North and South America
BiomeMap <- qtm(biomes_shp,
fill="biomes",
fill.style="fixed",
fill.labels=biomes_shp$biomes,
fill.palette=cols7,
fill.title="Biomes",
layout.legend.position=c("left","bottom"),
layout.legend.width=1.5,
layout.frame=FALSE)
BiomeMap
Figure 1. Map of North and South American biomes.
Beta Diversity Plots by Biome
BiomeBetaWeightBV <- ggplot(BiomeBetaCellsCentCov, aes(x=Type, y=Beta, fill=Type, color=Type)) +
geom_boxplot(show.legend = FALSE, fill=biome_cols_11, color="black") +
guides(x = guide_axis(angle=30)) +
#theme_minimal() + #un-comment whichever theme you want
theme_gray() +
#theme_light() +
#theme_bw() +
geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35,
color="gray25") +
xlab("Biome") +
ylab("Beta Diversity") +
theme(axis.title.y = element_text(size=22),
axis.title.x = element_text(size=22),
axis.text.y = element_text(size=16),
axis.text.x = element_text(angle = 30, hjust = 1, size = 16))
BiomeBetaWeightBV
Range Size Plots by Biome
BiomeRangeBV <- ggplot(BiomeRange, aes(x=Type, y=Range, fill=Type, color=Type)) +
geom_boxplot(show.legend = FALSE, fill=biome_cols_11, color="black") +
guides(x = guide_axis(angle=30)) +
#un-comment whichever theme you want
#theme_minimal() +
theme_gray() +
#theme_light() +
#theme_bw() +
geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35,
color="gray25") +
xlab("Biome") +
ylab("Range") +
theme(axis.title.y = element_text(size=22),
axis.title.x = element_text(size=22),
axis.text.y = element_text(size=20),
axis.text.x = element_text(angle = 30, hjust = 1, size = 16))
BiomeRangeBV
Alpha Diversity by Order, Split into Biomes
Orders with Maximum Alpha Diversity > 10
FacetOBRBelow10 <- ggplot(OBRBelow10DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) +
geom_boxplot(show.legend = FALSE, fill=biome_cols_166, color="black", outlier.size=0.7) +
#un-comment whichever theme you want
#theme_minimal() +
theme_gray() +
#theme_light() +
#theme_bw() +
#theme_dark() +
#theme_linedraw() +
#geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
xlab("Biome") +
ylab("Richness") +
theme(axis.title.y = element_text(size=22),
axis.title.x = element_text(size=22),
axis.text.y = element_text(size=15),
axis.text.x = element_text(angle = 90, hjust = 1, size = 12))+
facet_wrap(~Order,
#un-comment # of rows you want
ncol=6
#ncol=5
)
FacetOBRBelow10
Orders with Maximum Alpha Diversity between 10 and 25
FacetOBR10to25 <- ggplot(OBR10to25DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) +
geom_boxplot(show.legend = FALSE, fill=biome_cols_66, color="black", outlier.size=0.7) +
#un-comment whichever theme you want
#theme_minimal() +
theme_gray() +
#theme_light() +
#theme_bw() +
#theme_dark() +
#theme_linedraw() +
geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
xlab("Biome") +
ylab("Richness") +
theme(axis.title.y = element_text(size=22),
axis.title.x = element_text(size=22),
axis.text.y = element_text(size=15),
axis.text.x = element_text(angle = 45, hjust = 1, size = 12))+
facet_wrap(~Order,
#un-comment # of rows you want
ncol=3
#ncol=2
)
FacetOBR10to25
Orders with Maximum Alpha Diversity between 25 and 100
FacetOBR25to100 <- ggplot(OBR25to100DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) +
geom_boxplot(show.legend = FALSE, fill=biome_cols_87, color="black", outlier.size=0.7) +
#un-comment whichever theme you want
#theme_minimal() +
theme_gray() +
#theme_light() +
#theme_bw() +
#theme_dark() +
#theme_linedraw() +
geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
xlab("Biome") +
ylab("Richness") +
theme(axis.title.y = element_text(size=22),
axis.title.x = element_text(size=22),axis.text.y = element_text(size=15),
axis.text.x = element_text(angle = 30, hjust = 1, size = 10)) +
facet_wrap(~Order,
#un-comment # of rows you want
ncol=4
#ncol=2
)
FacetOBR25to100
Orders with Maximum Alpha Diversity > 100
FacetOBRAbove100 <- ggplot(OBRAbove100DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) +
geom_boxplot(show.legend = FALSE, fill=biome_cols_22, color="black", outlier.size=1) +
#un-comment whichever theme you want
#theme_minimal() +
theme_gray() +
#theme_light() +
#theme_bw() +
#theme_dark() +
#theme_linedraw() +
geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
xlab("Biome") +
ylab("Richness") +
theme(axis.title.y = element_text(size=22),
axis.title.x = element_text(size=22),
axis.text.y = element_text(size=15),
axis.text.x = element_text(angle = 45, hjust = 1, size = 12)) +
facet_wrap(~Order,
#un-comment # of rows you want
ncol=2
#ncol=1
)
FacetOBRAbove100
Circle Plots
Species richness for each order, grouped by biome
All bryophyte orders
circos.clear()
circos.par(start.degree = 0)
chordDiagram(CircleMatAll, grid.col = grid.col, column.col = biome_cols_11,
directional = 1, direction.type = "arrows", link.arr.type = "big.arrow",
link.arr.length = 0.05, link.largest.ontop = T, annotationTrack = c("grid"),
preAllocateTracks = 1, big.gap = 20, small.gap = 2)
circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim), ylim[1], sector.name, facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.5)
}, bg.border = NA)
Only moss orders
circos.clear()
circos.par(start.degree = 0)
chordDiagram(CircleMatAllMoss, grid.col = grid.col, column.col = biome_cols_11,
directional = 1, direction.type = "arrows", link.arr.type = "big.arrow",
link.arr.length = 0.05, link.largest.ontop = T, annotationTrack = c("grid"),
preAllocateTracks = 1, big.gap = 20, small.gap = 2)
circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
sector.name = get.cell.meta.data("sector.index")
circos.text(mean(xlim), ylim[1], sector.name, facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.5)
}, bg.border = NA)
